TOM'S driver Miyata came from 12th on the grid to pass Tsuboi around the outside of Turn 1 on the penultimate lap of the 31-lap race to seal his first win in the Japanese single-seater category.
Miyata had vaulted into contention thanks to a safety car period that was prompted when Nojiri and Oyu came to blows on the latter driver's out-lap, putting both in the barriers and out of the race.
Ryo Hirakawa made a late pass on Liam Lawson to finish third, completing an-all Toyota podium.
After an aborted start, owing to Dandelion Racing's Tadasuke Makino failing to get going from the grid, TGM Grand Prix poleman Oyu led the opening stages as Inging's Tsuboi and Nojiri settled into second and third places.
Lawson however was the driver on the move, jumping from eighth on the grid to fourth on the opening lap, and on the third lap he managed to clear Mugen team-mate Nojiri to move up to third.
Nojiri meanwhile appeared to be struggling, dropping another place to Kondo Racing man Kenta Yamashita.
When the pit window opened on lap 10, Lawson was first of the leaders to come in for his mandatory stop, followed by Tsuboi next time around.
Lawson came out behind Tsuboi and was unable to take advantage as the Inging driver got his tyres up to temperature.
Source: Autosport